Create TruSight Tumor 15 Sample Plates and Sample Sheets with IEM (1000000001314 v01)

Create TruSight Tumor 15 Sample Plates and Sample Sheets with IEM (1000000001314 v01)
Create TruSight Tumor 15 Sample Plates and Sample Sheets
with IEM
For Research Use Only. Not for use in diagnostic procedures.
This quick reference card describes how to use the Illumina®
Experiment Manager (IEM) to create a TruSight® Tumor 15
sample plate, and create and edit sample sheets compatible
with your Illumina sequencing system and analysis software.
For more detailed general information on how to use the IEM
application and definitions of the sample sheet applications,
see the Illumina Experiment Manager User Guide (Document #
15031335). New or less experienced users are advised to read
the guide before using this quick reference card.
}
}
}
If you want to copy an image of your sample plate for use
in a presentation or paper, select Copy to Clipboard on
the Plate Graphics tab.
You can paste the image into any graphics-enabled
program, such as Paint, Microsoft PowerPoint, Microsoft
Word, and Adobe Photoshop.
If you want to print an image of your sample plate, select
Print on the Plate Graphics tab.
10 Select Finish and save the sample plate file.
WARNING
The sample plate file must contain the *.amp26.plt file
extension.
Create a Sample Plate
1
Open the IEM software.
2
On the IEM main screen, select Create Sample Plate.
Create a MiSeq-Compatible Sample Sheet
3
From the Library Prep Kit list, select TruSight Tumor 15,
and then select Next.
1
On the IEM main screen, select Create Sample Sheet.
4
On the Assay Parameters screen, do the following:
2
On the Instrument Selection screen, select MiSeq, and
then select Next.
3
On the MiSeq Application Selection screen, select the
Targeted Resequencing category, and then select the
TruSight Tumor 15 application, and then select Next.
4
On the Workflow Parameters screen, do the following:
a
b
c
In the Unique Plate Name field, type a name for the
sample plate.
The Index Reads field is automatically set to 2.
Select Next.
5
On the Plate Samples screen, make sure that the Table tab
is selected.
6
For each well that contains a sample, Enter a unique
sample ID indicating the DNA source, and the TruSight
Tumor primer pool-specific indicator (either A or B). Each
unique DNA source must have both an A and B unique
pool sample ID. Make the sample name identical for the
matched pair.
Sample ID
Sample Name
Sample 1—Pool A
Sample001A
DNASample001
Sample 1—Pool B
Sample001B
DNASample001
7
Specify what unique set of index adapters you intend to
use for each well.
8
If you want to capture more detailed information about
the plate, enter a sample project and description.
9
[Optional] Select the Plate Graphic tab to view the sample
ID in each well.
Document # 1000000001314 v01
a
b
c
d
e
f
g
5
Add sample information to the sample sheet. Choose from
the following:
a
b
6
In the Reagent Cartridge Barcode field, enter the
barcode number of the MiSeq reagent cartridge.
The Index Reads field is automatically set to 2.
[Optional] Type an experiment name, investigator
name, and description.
Select the date.
The read type is automatically set to Paired End.
The number of cycles for each read is automatically
set to 151.
Select Next.
To import an existing sample plate, proceed to step 6.
To add new sample information, proceed to step 7.
Import an existing sample plate.
a
On the Sample Selections screen, clear the Maximize
checkbox to display the Sample Plate area.
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Create TruSight Tumor 15 Sample Plates and Sample Sheets with IEM
b
c
d
e
7
Select Select Plate and navigate to a sample plate you
created previously.
Select Select All to include all wells in this sequencing
run or highlight the wells you want to include in this
sequencing run.
Select Add Selected Samples.
Select Finish and save the sample sheet file.
Add new sample information.
} On the Sample Selection screen, select Add Blank Row
to add rows and manually enter the sample
information. There are 2 rows per DNA sample, 1 for
each library pool, A and B.
} Enter a unique sample ID indicating the DNA source,
and the TruSight Tumor primer pool-specific indicator
(either 'A' or 'B'). Each unique DNA source must have
both an A and B unique pool sample ID. Make the
sample name identical for the matched pair.
Sample ID
Sample Name
Sample 1—Pool A
Sample001A
DNASample001
Sample 1—Pool B
Sample001B
DNASample001
Copyright and Trademarks
© 2015 Illumina, Inc. All rights reserved.
Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse,
BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, ForenSeq,
Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X,
Infinium, iScan, iSelect, MiSeq, MiSeqDx, MiSeq FGx, NeoPrep,
NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome,
TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi,
VeriSeq, the pumpkin orange color, and the streaming bases design are
trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other
countries. All other names, logos, and other trademarks are the property of
their respective owners.
} Select the Index1 (I7) and Index2 (I5) indexes from the
drop-down list in each cell. The index pair must be
unique for each well.
} Select the appropriate Manifest file (containing targeted
amplicon regions) for each pair of A and B primer pool
samples. For A pools, select TST_15-A-Manifest; for B
pools, select TST_15-B-Manifest.
} Optional fields include Plate, Well, and Sample Project.
} Select Finish and save the sample sheet file.
Create a BaseSpace-Compatible Sample Sheet
1
Enter sample IDs that include the sample name and
manifest. For example: Library1-SampleName-A and
Library2-SampleName-B.
2
Create a separate BaseSpace Project for each sequencing
run to simplify sample selection during analysis. Leave
the Project field blank in the sample sheet to create a
BaseSpace Project folder named with the Run ID.
Technical Assistance
For questions, see Illumina Experiment Manager on
www.illumina.com. If you do not find the information you
need there, contact Illumina Technical Support by email or
phone.
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Document # 1000000001314 v01
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